Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

Just an FYI, not sure if it's relevant or not: I have not yet done an rdkit build with boost 1.51, so I am not sure that the problem isn't there -greg On Tuesday, October 9, 2012, George Papadatos wrote: > Hi James, > > You're right. I checked out the true HEAD which is 2234 but it still > fail

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

My apology. The homebrew formula was using the old svn repo. (I thought sourceforge would do a redirect automatically from the old repo.) It has been fixed. Try these and see if it works: brew untap edc/homebrew-rdkit brew tap edc/homebrew-rdkit brew rm rdkit brew fetch --HEAD rdkit --force -v

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

homebrew is using the old svn repo? On 09/10/12 22:33, James Swetnam wrote: George- My templating fix was submitted as 2155, and HEAD in SVN is at 2234. I'm not terribly familiar with homebrew, or why it thinks 2148 is HEAD James On Tue, Oct 9, 2012 at 2:27 PM, George Papadatos

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

Hi James, You're right. I checked out the true HEAD which is 2234 but it still failed! This is the make log: MS-Verdun:build georgep$ cmake -D PYTHON_LIBRARY=/${PYTHON_ROOT}/Python -DPYTHON_INCLUDE_DIR=${PYTHON_ROOT}/Headers .. 2>&1 | tee cmake.log -- The C compiler identification is GNU 4.2.1 -

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

George- My templating fix was submitted as 2155, and HEAD in SVN is at 2234. I'm not terribly familiar with homebrew, or why it thinks 2148 is HEAD James On Tue, Oct 9, 2012 at 2:27 PM, George Papadatos wrote: > Hi James, > > Many thanks for the quick answer. I'm afraid I'm already using the t

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

Hi James, Many thanks for the quick answer. I'm afraid I'm already using the trunk: brew install -v --HEAD rdkit --with-inchi (revision 2148) Regards, George On 9 October 2012 21:30, James Swetnam wrote: > George- > > I believe you're running into an issue that was raised on the developer >

[Rdkit-discuss] neutralize charges

Is there anything in RDKit to neutralize charges, like what Corina does with the 'neu' option? Quoting from the Corina documentation: • The new option -d neu neutralizes formal charges at acids, alcoholates, and basic nitrogens by adding or removing protons. Often it is useful

Re: [Rdkit-discuss] problems with RDKit and Mountain Lion

George- I believe you're running into an issue that was raised on the developer list. I submitted a patch for this issue, which has been applied in the SVN trunk. If you install from trunk you should be fine. Best James On Tue, Oct 9, 2012 at 12:52 PM, George Papadatos wrote: > HI RDKitters,

[Rdkit-discuss] problems with RDKit and Mountain Lion

HI RDKitters, I get compilation errors when I try to build RDKit on a new Mountain Lion Mac OS machine. I've tried both Eddie's brew formula and manual installation with cmake. I also tried both the beta 2012_09 versions and the 2012_06 one. Apart from the system python, I use the python.org versi

[Rdkit-discuss] ForwardSDMolSupplier::atEnd bug

Hi, Working in C++, I am calling ForwardsSDMolSupplier's method "atEnd()", expecting that it returns false if there are more molecules and true if there are no more molecules. As such the line: while (!molSupplier->atEnd()) ought to be the obvious looping test with molSupplier->next()

Re: [Rdkit-discuss] fdef files

Hi James, Yes – I just checked the files I generated for the ph4 definitions and they definitely do not have the tautomer recognition (guess I am just not SMART enough for this ;-). I will follow up with Greg and see how quickly we can get the fdef file as a contribution so people can start to a

Re: [Rdkit-discuss] parallel conformation generation

This is great Andrew (especially the subsequent explanation)! Many Thanks. Considering that this is a task lots of people will want to do - is this code CONTRIB dir material? (perhaps max_workers should be a fourth command line argument defaulting to 1) A few months (years?) back Greg suggested